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Conserved domains on  [gi|371560283|gb|AEX36926|]
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DNA-directed RNA polymerase subunit beta, partial [Sphingomonas sp. 505]

Protein Classification

DNA-directed RNA polymerase subunit beta( domain architecture ID 1000195)

DNA-directed RNA polymerase subunit beta catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

CATH:  3.90.1110.10
EC:  2.7.7.6
Gene Ontology:  GO:0000428|GO:0003899|GO:0006351
PubMed:  6266829
SCOP:  4003708

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-359 0e+00

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 820.11  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:PRK00405  426 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEY 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKATDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVSVA 159
Cdd:PRK00405  506 GFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLdEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  160 AALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRAtNESDARR 239
Cdd:PRK00405  586 ASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGE 664

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  240 SGVDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIVRD 319
Cdd:PRK00405  665 DGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKE 744

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560283  320 EVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:PRK00405  745 DVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 784
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-359 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 820.11  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:PRK00405  426 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEY 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKATDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVSVA 159
Cdd:PRK00405  506 GFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLdEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  160 AALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRAtNESDARR 239
Cdd:PRK00405  586 ASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGE 664

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  240 SGVDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIVRD 319
Cdd:PRK00405  665 DGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKE 744

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560283  320 EVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:PRK00405  745 DVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 784
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-359 0e+00

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 724.53  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283     1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:TIGR02013  381 FFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEY 460

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    81 GFIESPYRRVKDGKA--TDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVS 157
Cdd:TIGR02013  461 GFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLdENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVS 540

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   158 VAAALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRATNESDA 237
Cdd:TIGR02013  541 VAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEE 620

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   238 RRSGVDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIV 317
Cdd:TIGR02013  621 PDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLV 700

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 371560283   318 RDEVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:TIGR02013  701 KDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNL 742
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-359 0e+00

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 630.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:COG0085   365 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEY 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKATDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVSVA 159
Cdd:COG0085   445 GFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLdEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVA 524

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  160 AALIPFLENDDANRALMGANMQRQAVPLVQSDAPLvgtgmeavvavdsgavvvarrdgvveqidgtrivvratnesdarr 239
Cdd:COG0085   525 TSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL--------------------------------------------- 559

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  240 sgvDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIVRD 319
Cdd:COG0085   560 ---LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKD 636

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560283  320 EVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:COG0085   637 DVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 676
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-359 1.12e-100

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 316.05  E-value: 1.12e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   1 FFGSSQ------------LSQFMDQTNPLSEITHKRRLSAlgpGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLI 68
Cdd:cd00653  295 FLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  69 NSLATHARVNkyGFIESPYRRVKDgkatdqvvyisameeakytiaqanielkdgmiveelvpgringdsqlliraDVDMM 148
Cdd:cd00653  372 KNLALMARIS--GRIERPYRIVEK---------------------------------------------------EVTHI 398

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283 149 DVSPKQVVSVAAALIPFLENDDANRALMGANMQRQAVPlvqsdaplvgtgmeavvavdsgavvvarrdgvveqIDGTRIV 228
Cdd:cd00653  399 EISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG-----------------------------------TPALNQQ 443

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283 229 VRATNEsdarrsgvdIYRLSKfqrsnqstciNQRPIVRVGDEVKVGdviadgpstdLGELALGRNALVAFMPWNGYTFED 308
Cdd:cd00653  444 YRMDTK---------LYLLLY----------PQKPLVGTGIEEYIA----------FGELPLGQNAIVAVMSYSGYNFED 494

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 371560283 309 SILISERIVRDEVFTSIHIEEFEVMARDTKLGPEEITR-DIPNVGEEALRNL 359
Cdd:cd00653  495 AIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNL 546
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 212-359 1.63e-50

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 172.71  E-value: 1.63e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  212 VARRDGVVEQIDGTRIVVRATNESDArrsgVDIYRLSKFQRSNQST---CINQRPIVRVGDEVKVgdviadgpstDLGEL 288
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQA----MGIYTLNKFYRSDQNTyvlCYPQKPLVKTGAVEAG----------GFGEL 66

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 371560283  289 ALGRNALVAFMPWNGYTFEDSILISERIVRDEVFTSIHIEEFEvmARDTKLGP-EEITRDIPNVGEEALRNL 359
Cdd:pfam00562  67 PLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKL 136
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-359 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 820.11  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:PRK00405  426 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEY 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKATDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVSVA 159
Cdd:PRK00405  506 GFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLdEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  160 AALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRAtNESDARR 239
Cdd:PRK00405  586 ASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGE 664

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  240 SGVDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIVRD 319
Cdd:PRK00405  665 DGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKE 744

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560283  320 EVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:PRK00405  745 DVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 784
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-359 0e+00

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 724.53  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283     1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:TIGR02013  381 FFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEY 460

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    81 GFIESPYRRVKDGKA--TDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVS 157
Cdd:TIGR02013  461 GFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLdENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVS 540

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   158 VAAALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRATNESDA 237
Cdd:TIGR02013  541 VAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEE 620

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   238 RRSGVDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIV 317
Cdd:TIGR02013  621 PDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLV 700

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 371560283   318 RDEVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:TIGR02013  701 KDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNL 742
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-359 0e+00

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 630.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:COG0085   365 FFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEY 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKATDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVSVA 159
Cdd:COG0085   445 GFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLdEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVA 524

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  160 AALIPFLENDDANRALMGANMQRQAVPLVQSDAPLvgtgmeavvavdsgavvvarrdgvveqidgtrivvratnesdarr 239
Cdd:COG0085   525 TSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL--------------------------------------------- 559

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  240 sgvDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIVRD 319
Cdd:COG0085   560 ---LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKD 636

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560283  320 EVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:COG0085   637 DVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNL 676
rpoB CHL00001
RNA polymerase beta subunit
 1-359 2.03e-173

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 510.60  E-value: 2.03e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:CHL00001  368 FFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHW 447

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKATDQVVYISAMEEAKYTIAQAN-IELKDGMIVEELVPGRINGDSqLLIRAD-VDMMDVSPKQVVSV 158
Cdd:CHL00001  448 GSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNsLALNQGIQEEQVVPARYRQEF-LTIAWEqIHLRSIFPFQYFSI 526

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  159 AAALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRATNEsdar 238
Cdd:CHL00001  527 GASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGD---- 602

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  239 rsgVDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIVR 318
Cdd:CHL00001  603 ---TLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVY 679

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 371560283  319 DEVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:CHL00001  680 EDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNL 720
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-359 3.51e-168

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 519.95  E-value: 3.51e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:PRK14844  526 FFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKY 605

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKATDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVSVA 159
Cdd:PRK14844  606 GFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLdENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVA 685

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  160 AALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRATNESDARR 239
Cdd:PRK14844  686 ASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNY 765

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  240 SGVDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIVRD 319
Cdd:PRK14844  766 LDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKK 845

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560283  320 EVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:PRK14844  846 DLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHL 885
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-359 3.29e-164

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 486.91  E-value: 3.29e-164
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:CHL00207  360 FFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKF 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKA--TDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVS 157
Cdd:CHL00207  440 GFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLnKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFS 519

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  158 VAAALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRatnesDA 237
Cdd:CHL00207  520 IAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQ-----DD 594

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  238 RRSGVdIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIV 317
Cdd:CHL00207  595 NNRYI-HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLV 673

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 371560283  318 RDEVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:CHL00207  674 YEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNL 715
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-359 7.84e-163

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 504.84  E-value: 7.84e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    1 FFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKY 80
Cdd:PRK09603  519 FFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDL 598

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   81 GFIESPYRRVKDGKATDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVSPKQVVSVA 159
Cdd:PRK09603  599 GFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIdEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVA 678

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  160 AALIPFLENDDANRALMGANMQRQAVPLVQSDAPLVGTGMEAVVAVDSGAVVVARRDGVVEQIDGTRIVVRATNESDARr 239
Cdd:PRK09603  679 ASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEAY- 757

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  240 sgVDIYRLSKFQRSNQSTCINQRPIVRVGDEVKVGDVIADGPSTDLGELALGRNALVAFMPWNGYTFEDSILISERIVRD 319
Cdd:PRK09603  758 --IDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKD 835

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 371560283  320 EVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNL 359
Cdd:PRK09603  836 DIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHL 875
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-359 1.12e-100

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 316.05  E-value: 1.12e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283   1 FFGSSQ------------LSQFMDQTNPLSEITHKRRLSAlgpGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLI 68
Cdd:cd00653  295 FLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  69 NSLATHARVNkyGFIESPYRRVKDgkatdqvvyisameeakytiaqanielkdgmiveelvpgringdsqlliraDVDMM 148
Cdd:cd00653  372 KNLALMARIS--GRIERPYRIVEK---------------------------------------------------EVTHI 398

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283 149 DVSPKQVVSVAAALIPFLENDDANRALMGANMQRQAVPlvqsdaplvgtgmeavvavdsgavvvarrdgvveqIDGTRIV 228
Cdd:cd00653  399 EISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG-----------------------------------TPALNQQ 443

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283 229 VRATNEsdarrsgvdIYRLSKfqrsnqstciNQRPIVRVGDEVKVGdviadgpstdLGELALGRNALVAFMPWNGYTFED 308
Cdd:cd00653  444 YRMDTK---------LYLLLY----------PQKPLVGTGIEEYIA----------FGELPLGQNAIVAVMSYSGYNFED 494

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 371560283 309 SILISERIVRDEVFTSIHIEEFEVMARDTKLGPEEITR-DIPNVGEEALRNL 359
Cdd:cd00653  495 AIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNL 546
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 212-359 1.63e-50

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 172.71  E-value: 1.63e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283  212 VARRDGVVEQIDGTRIVVRATNESDArrsgVDIYRLSKFQRSNQST---CINQRPIVRVGDEVKVgdviadgpstDLGEL 288
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQA----MGIYTLNKFYRSDQNTyvlCYPQKPLVKTGAVEAG----------GFGEL 66

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 371560283  289 ALGRNALVAFMPWNGYTFEDSILISERIVRDEVFTSIHIEEFEvmARDTKLGP-EEITRDIPNVGEEALRNL 359
Cdd:pfam00562  67 PLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKL 136
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 9-76 5.23e-40

RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 135.73  E-value: 5.23e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 371560283    9 QFMDQTNPLSEITHKRRLSAlGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHAR 76
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 87-151 4.00e-25

RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.


Pssm-ID: 463067 [Multi-domain]  Cd Length: 66  Bit Score: 96.28  E-value: 4.00e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 371560283   87 YRRVKDGKATDQVVYISAMEEAKYTIAQANIEL-KDGMIVEELVPGRINGDSQLLIRADVDMMDVS 151
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLdEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 8-77 9.31e-20

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 90.79  E-value: 9.31e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560283    8 SQFMDQTNPLSEITHKRRLsaLGPggLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARV 77
Cdd:PRK08565  403 SQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI 468
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 3-79 2.24e-18

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 86.16  E-value: 2.24e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 371560283   3 GSSQLSQFMDQTNPLSEITHKRRLSAlgpgGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNK 79
Cdd:PRK09606 401 GRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEIST 473
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 208-281 9.52e-03

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 38.12  E-value: 9.52e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 371560283  208 GAVVVARRDGVVEQI---DGTRIVVRATNESDARRsgvdiYRLSKfqrsnqstciNQRPIVRVGDEVKVGDVIADGP 281
Cdd:PRK00566  927 GPAIIAEIDGTVSFGketKGKRRIVITPDDGEERE-----YLIPK----------GKHLLVQEGDHVEAGDKLTDGS 988
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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